We are currently carrying out a series of molecular dynamics simulation on the HIV-1 protease. In these preliminary studies, we are examining the interactions between the substrate and the protein in a solvated system. In future simulations, we will examine in detail, the behavior of the flap regions to try to identify their role in specificity. By varying the substrate, we hope to be able to identify the key interactions which account for the specificity of this protease. We anticipate collaborating with a pharmaceutical company so that ideas that derive from the analysis of the simulations can be tested experimentally.